GLENDALE, Arizona (Reuters) - The New England Patriots rallied to beat the Seattle Seahawks on Sunday in what will go down as one of the greatest Super Bowls of all-time but who the real winner is could well be debated for decades to come.

The buildup to the Super Bowl had been dominated by a controversy over deflated footballs used by the Patriots in a blowout win over the Indianapolis Colts in the AFC title game that earned them a trip to Arizona.

A whiff of scandal continued to hang over Sunday’s game even as the Vince Lombardi Trophy was hoisted and confetti fell from the roof of the University of Phoenix Stadium still trembling from New England’s heart-stopping win.

”We won that (AFC) game 45-7, we won today 28-24,“ defended a defiant Patriots owner Robert Kraft through the celebratory din. ”Our people didn’t touch the balls. I love our team, I‘m proud of our guys.

”We’re going to carry on and hopefully continue to do well.

”Every year if you’re privileged to get to this game, hard things happen. I‘m so proud of (Tom) Brady and (coach Bill) Belichick for handling things the way they did.

“I love them. And all our Patriots fans should feel very good.”

As the NFL’s investigation into “Deflategate” continues, the spotlight of suspicion remains firmly fixed on the Patriots with some fans even questioning why New England was allowed to play in the Super Bowl at all.

The controversy has dominated the sport headlines for two weeks and left stains on one of the NFL’s most successful franchises and two possible future Hall of Famers quarterback Brady and coach Belichick.

In the 20 years since Kraft bought the franchise, the Patriots have made the playoffs an eyebrow-raising 15 times and played in seven Super Bowls winning four.

BRADY MILESTONES

A battling Brady spent Sunday rewriting the Super Bowl quarterbacking record books, setting new marks for single-game completions (37), most career passing yards (1,605) and career touchdowns (13) to claim a third most valuable player award.

“It’s just a lot of mental toughness, I think the whole team had it,” said Brady when asked how the team was able to deal with the controversy and focus on the game. “Coach always says, ignore the noise and control what you can control.”

But the Patriots and Belichick, the only coach to take a team to six Super Bowls, have also developed a reputation as a team not above a bit of skullduggery.

In 2007, Belichick was fined $500,000 and the Patriots lost a first-round draft pick after an investigation found New England had videotaped an opponent’s signals on the sidelines in what became known as ‘Spygate’.

‘Deflategate’, however is unlikely to take any of the air out of the Super Bowl party and parade in Boston where the team will return home to a hero’s welcome.

“Congratulations to Patriots and all of Patriot Nation on a well earned Super Bowl victory. You have made Boston and New England proud - cue the duck boats!” said Boston mayor Marty Walsh.

He would lay out plans on Monday for a celebratory parade featuring the city’s signature “duck boats”, amphibious vehicles dating back to World War II.

The game represented a last chance for the NFL to put a scandal-scarred season behind it, and the Patriots and Seahawks did their part, providing a game that produced edge-of-the-seat excitement.

”I‘m not really concerned about that (controversy),“ said Belichick. ”I’ve already spoken on that, so I am not going to have anything to add to it.

”I‘m happy for our team. We won. I think our team deserved to win.

”We won tonight in a tough game. I don’t know what more we need to do.